Density functional studies of closed-shell attractions of S(AuPH3)2 and HS(AuPH3)2 + and their dimers.

abstract：:The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this a...

journal_title：Journal of molecular modeling

authors： Goraczko AJ,Szewczykowska K

更新日期：2009-06-01 00:00:00

abstract：:Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the developm...

journal_title：Journal of molecular modeling

authors： Mansourian M,Madadkar-Sobhani A,Mahnam K,Fassihi A,Saghaie L

更新日期：2012-09-01 00:00:00

abstract：:In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (βt) were calculated f...

journal_title：Journal of molecular modeling

authors： Paschoal D,Santos HF

更新日期：2013-05-01 00:00:00

abstract：:The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution ...

journal_title：Journal of molecular modeling

authors： Tian X,Jiang L,Yuan Y,Wang M,Guo Y,Zeng X,Li M,Pu X

更新日期：2013-06-01 00:00:00

abstract：:We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...

journal_title：Journal of molecular modeling

authors： Goldwaser E,de Courcy B,Demange L,Garbay C,Raynaud F,Hadj-Slimane R,Piquemal JP,Gresh N

更新日期：2014-11-01 00:00:00

abstract：:CO2 reduction has attracted extensive attentions for its wide applications in chemical engineering and green chemistry. As one of major commercial catalysts, Cu have been widely studied considering its low price and high catalytic efficiency. However, previous studies were mostly focused on the Cu(111) surface, while ...

journal_title：Journal of molecular modeling

authors： Wang R,Zhu B,Zhang G,Gao Y

更新日期：2020-07-09 00:00:00

abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

journal_title：Journal of molecular modeling

authors： Xia J,Li J,Sun H

更新日期：2012-04-01 00:00:00

abstract：:A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for π-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C6 moieties. Møller-Plesset (MP2, SCS-MP2) and coupled clu...

journal_title：Journal of molecular modeling

authors： Yurtsever E

更新日期：2015-01-01 00:00:00

abstract：:Understanding the structure and properties at the electrolyte-electrode interface is vital for the rational design of the supercapacitors or other electrochemical devices. In this work, we explored the influence of interlayer spacing of the MoS2 electrode on the interfacial structure and electrical properties of sodiu...

journal_title：Journal of molecular modeling

authors： Wang M,Wang Y,Li M,Wang S,He H

更新日期：2021-01-18 00:00:00

abstract：:Two uridine 2',3'-cyclic monophosphate (cUMP) derivatives, 5'-deoxy (DcUMP) and 5'-O-methyl (McUMP), were studied by means of quantum chemical methods. Aqueous solvent effects were estimated based on the isodensity-surface polarized-continuum model (IPCM). Gas phase calculations revealed only slight energy differences...

journal_title：Journal of molecular modeling

authors： Grabarkiewicz T,Hoffmann M

更新日期：2006-01-01 00:00:00

abstract：:Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influ...

journal_title：Journal of molecular modeling

authors： Sun YC,Hsu WC,Hsu CJ,Chang CM,Cheng KH

更新日期：2015-11-01 00:00:00

abstract：:In the present work, conformational analysis of lignin models was accomplished by considering four cross-link types (3-5', β-5', α-O-4 and β-O-4) and three monomer units [guaiacyl (G), p-hydroxyphenyl (H) and syringyl (S)]. Analysis involving the 3-5' and β-5' dimers was conducted following the standard procedure, i.e...

journal_title：Journal of molecular modeling

authors： Castilho-Almeida EW,De Almeida WB,Dos Santos HF

更新日期：2013-05-01 00:00:00

abstract：:The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

journal_title：Journal of molecular modeling

authors： Huo S,Meng D,Zhang X,Meng L,Li X

更新日期：2014-10-01 00:00:00

abstract：:The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an atta...

journal_title：Journal of molecular modeling

authors： Lan G,Jin S,Wang D,Li J,Lu Z,Jing B,Li L

更新日期：2018-07-02 00:00:00

abstract：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

journal_title：Journal of molecular modeling

authors： Wimmerová M,Mishra NK,Pokorná M,Koca J

更新日期：2009-06-01 00:00:00

abstract：:The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...

journal_title：Journal of molecular modeling

authors： Yin PG,Li QS

更新日期：2004-02-01 00:00:00

abstract：:Modulation of γ-aminobutyric acid (GABA) levels has been required in various disorders. GABA itself cannot be directly introduced into central nervous system (CNS) because of the blood brain barrier; inhibition of GABA aminotransferase (GABA-AT), which degrades GABA in CNS, has been the target for the modulation of GA...

journal_title：Journal of molecular modeling

authors： Park JY,Lee Y,Lee HJ,Kwon YS,Chun W

更新日期：2020-08-11 00:00:00

abstract：:Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...

journal_title：Journal of molecular modeling

authors： Kupka T,Buczek A,Broda MA,Stachów M,Tarnowski P

更新日期：2016-05-01 00:00:00

abstract：:Prion diseases are associated with misfolding and aggregation of prion protein (PrP). Cellular prion protein contains a disulfide bond linking Cys residues at positions 179 and 214. It has been proposed that this disulfide bond plays an important role in the conversion between cellular (PrP(C)) and the scrapie form of...

journal_title：Journal of molecular modeling

authors： Ning L,Guo J,Jin N,Liu H,Yao X

更新日期：2014-02-01 00:00:00

abstract：:Realistic molecular models of one and two-centre catalytic active sites originating from the cleavage of a precursor material known to give rise to an active double metal cyanide catalyst are described. Via periodic density functional calculations the structure of the proposed catalytic sites are shown to be dependent...

journal_title：Journal of molecular modeling

authors： Wojdeł JC,Bromley ST,Illas F,Jansen JC

更新日期：2007-07-01 00:00:00

abstract：:The structures, energetics, as well as several important chemical parameters, of antiretroviral drugs - nucleoside reverse transcriptase inhibitors (NRTIs) - and natural deoxyribonucleosides in both neutral, and positively and negatively charged states, are investigated. These studies are carried out within the frame ...

journal_title：Journal of molecular modeling

authors： Kumar V,Kishor S,Ramaniah LM

更新日期：2012-08-01 00:00:00

abstract：:The complexes formed between TX3-ZX2 (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH3 were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX3-ZX2, two types of complex were obtained. For CX3-ZX2, NH3 is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX3-ZX2 (T = Si and Ge), however, t...

journal_title：Journal of molecular modeling

authors： Li Y,Xu Z

更新日期：2018-08-20 00:00:00

abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

journal_title：Journal of molecular modeling

authors： Meiselbach H,Horn AH,Harrer T,Sticht H

更新日期：2007-02-01 00:00:00

abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...

journal_title：Journal of molecular modeling

authors： Gao HF,Zhang SH,Ren FD,Gou RJ,Han G,Wu JB,Ding X,Zhao WH

更新日期：2016-05-01 00:00:00

abstract：:In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2017-08-22 00:00:00

abstract：:The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 and Z-DNAs in different sequence contexts can affect many...

journal_title：Journal of molecular modeling

authors： Wang Q,Li L,Wang X,Liu H,Yao X

更新日期：2014-11-01 00:00:00

abstract：:The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of thr...

journal_title：Journal of molecular modeling

authors： Minovski N,Perdih A,Solmajer T

更新日期：2012-05-01 00:00:00

abstract：:Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296 K, as well as three different crystal faces, (001), (120), and (010). When t...

journal_title：Journal of molecular modeling

authors： Shi L,Duan XH,Zhu LG,Pei CH

更新日期：2020-01-11 00:00:00

abstract：:We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

journal_title：Journal of molecular modeling

authors： Kayi H,Clark T

更新日期：2011-10-01 00:00:00

abstract：:Ethanol and water are the solvents most commonly used to extract flavonoids from propolis. Do hydrogen-bonding interactions exist between flavonoids and ethanol/water? In this work, this question was addressed by using density functional theory (DFT) to provide information on the hydrogen-bonding interactions between ...

journal_title：Journal of molecular modeling

authors： Zheng YZ,Zhou Y,Liang Q,Chen DF,Guo R

更新日期：2016-04-01 00:00:00